Yup, that's how Bitcoin works. So what? SD paid a transaction fee to do that.
No, it's not how Bitcoin works. When you send an ordinary transaction, it's outputs only need to stay in the block chain while they are unspent. After someone spends the entire output, it can be pruned (removed from disk). Until that point it needs to stay in long term storage. Single-satoshi outputs would cost more in fees to send than the amount of the output, which is why no sane person would ever spend such an amount. For this reason they effectively can never be pruned.
Yea, it is how Bitcoin works. That's exactly WHY it works. Bitcoin is a protocol. Pruning is a client implementation. Does this make pruning techniques less efficient, yup sure does.